Upload corpus360M[multi-species]-model170M/config.yaml with huggingface_hub
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corpus360M[multi-species]-model170M/config.yaml
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model:
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name: ContrastiveModel
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dim_hid: 2048
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dropout: 0.1
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nlayers: 16
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num_head: 16
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training:
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lr: 0.0001
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min_lr: 0
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warmup: 20000
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devices: -1
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max_steps: 4000000
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num_nodes: 1
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scheduler: warmup
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accelerator: gpu
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masking_rate: 0
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weight_decay: 0.01
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optimizer_class: AdamW
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train_vocab_only: false
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gradient_clip_val: 1
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log_every_n_steps: 1000
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val_check_interval: 25000
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limit_train_batches: 1
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resume_from_checkpoint: false
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accumulate_grad_batches: 1
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check_val_every_n_epoch: null
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use_learnable_embs_freq: 0.8
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validate_before_training: false
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freeze_pretrained_vocabulary: true
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cls_value: -2
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dim_model: 1024
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activation: gelu
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mask_value: -1
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pe_max_len: 25000
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norm_scheme: pre
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decoder_head: false
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dim_gene_embs: 1024
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input_encoding: rank_encoding
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projection_dim: null
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flash_attention: true
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mlm_loss_weight: 0
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cont_loss_weight: 1
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contrastive_loss: multiclass
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loss_switch_step: 20000
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dim_pretrained_vocab: 640
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logit_scale_init_value: 3
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values_only_sanity_check: false
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data_loading_speed_sanity_check: false
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profiler:
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enabled: false
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datamodule:
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name: DataModule
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dataset:
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train:
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max_tokens: 20000
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qc_threshold: 1.0e-05
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panel_overlap: false
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panel_size_max: 60000
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panel_size_min: 400
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panel_selection: mixed
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panel_filter_regex: .*
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panel_max_drop_rate: 0.5
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max_total_seq_length: 80000
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feature_max_drop_rate: null
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panel_selection_mixed_prob: 0.25
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species:
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- hsapiens
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- mmusculus
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- cjacchus
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- mmulatta
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- ptroglodytes
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- btaurus
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- celegans
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- drerio
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- dmelanogaster
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- ecaballus
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- ggallus
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- ggorilla
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- hgfemale
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- ocuniculus
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- oaries
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- sscrofa
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obs_keys:
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- dataset
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- donor_id
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- tissue
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- cell_type
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dataloader:
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train:
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shuffle: true
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drop_last: true
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batch_size: 512
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num_groups: null
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pin_memory: true
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num_samples: null
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num_workers: 2
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within_group_sampling: dataset
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normalization: raw
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precomp_embs_key: null
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gene_sampling_strategy: top-nonzero
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model_speed_sanity_check: false
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initialize:
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resume: true
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run_id: s3z512hv
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checkpoint: latest/last.ckpt
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create_new_run: true
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